%\VignetteIndexEntry{Entrez Genome queries}

\documentclass[12pt]{article}

\usepackage{Sweave}
\usepackage{fullpage}
\usepackage{hyperref}

\newcommand{\R}{\textsf{R}}
\newcommand{\Rcmd}[1]{\texttt{#1}}
\newcommand{\pkg}[1]{\texttt{#1}}

\title{ Entrez database queries  }
\author{Chris Stubben}

\begin{document}
\maketitle


%% for cutting and pasting use continue =""
%% change margins on every chunk
<<setup, echo=FALSE>>=
library(genomes)
data(lproks)
options(warn=-1, width=75, digits=2, scipen=3,  "prompt" = "R> ", "continue" = " ")
options(SweaveHooks=list(fig=function() par(mar=c(5,4.2,1,1))))
@



Genome tables may also be created using two Entrez Utility functions.  The \Rcmd{term2summary}
function remotely queries the Genome Project database at NCBI using
any valid combination of Entrez search terms and returns a genome
table.  Since detailed taxonomy information is not stored in the local
tables, a typical search may include listing genomes projects by a
taxonomy group like family, class or order. In addition, some fields
in the genome tables like sequencing center may be incomplete and many
other fields are missing.  For example, this query returns a list of
microbial genome projects which have sequence data in the Short Read
Archive.


<<esum, keep.source=TRUE>>=
sra <- term2summary("genomeprj sra[Filter] AND Bacteria[ORGN]")
sra
@ 


The \Rcmd{term2neighbor} function searches the Genome database and
retrieves links to other genomes for a species (genome neighbors) in
the Nucleotide database and then returns a table listing accession
numbers, deflines, released dates, and taxonomy ids. Viral genomes
typically have one Reference sequence per species, and other strains
are linked as Genome Neighbors.  For example, Nipah virus is listed
once in the virus table (NC\_002728) and has 7 neighbors reported.  To
download those 7 neighbors, use the \Rcmd{term2neighbor} function
shown in the next example.  In addition, the function can also return
the GenBank sequence that the reference was derived from using the
\Rcmd{derived=TRUE} option.

Finally, if you are searching for a large group of viruses, it is often helpful to lookup the
scientific name using the taxonomy ID in the table.  The \Rcmd{taxid2names}
function takes a taxonomy ID and returns the scientific name and
lineage from the Taxonomy database.  Using pattern matching, one can return
the genus and plot released dates. 


<<eneigh, fig=TRUE, include=FALSE, height=4, width=4>>=
data(virus)
subset(virus, name %like% 'Nipah*')
nipah<-term2neighbor('Nipah virus[orgn]')
nipah[,1:2]

buny<- term2neighbor("Bunyaviridae[ORGN]", derived=TRUE)
nrow(buny)
taxids<-unique(buny$taxid)
btax<- taxid2names(taxids)
genus<-gsub("(.*Bunyaviridae; )(\\w*)(.*)", "\\2", btax$lineage)
n<-match(buny$taxid, btax$taxid)
plotby(buny, genus[n], log='y', lbty='n', lcex=.7)

@ 

\begin{figure}[t]
\centering
\includegraphics[height=3in,width=3in]{entrez-queries-eneigh.pdf}
 \caption{Accumulated number of genome sequences for vector-borne viruses in the family Bunyaviridae.}
\label{eneigh}
\end{figure}



\end{document}